BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716418.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 987,940 number of mapped reads = 887,616 (89.85%) number of supplementary alignments = 4,197 (0.42%) number of secondary alignments = 0 number of mapped bases = 51,320,008 bp number of sequenced bases = 51,305,962 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,534 duplication rate = 1.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3191 >>>>>>> ACTG content number of A's = 12,368,872 bp (24.11%) number of C's = 9,860,704 bp (19.22%) number of T's = 16,173,005 bp (31.52%) number of G's = 12,902,682 bp (25.15%) number of N's = 699 bp (0%) GC percentage = 44.37% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 254,828 number of insertions = 3,319 mapped reads with insertion percentage = 0.37% number of deletions = 8,968 mapped reads with deletion percentage = 1% homopolymer indels = 43.88% >>>>>>> Coverage mean coverageData = 0.0166X std coverageData = 0.1667X There is a 1.54% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5724429 0.02296655862694922 0.2523302937549786 chr2 243199373 4599589 0.018912832476751493 0.21103221051502097 chr3 198022430 5230957 0.0264159822702913 0.17264196368486293 chr4 191154276 2206094 0.011540908454488352 0.11933274074870208 chr5 180915260 2081029 0.011502783126199526 0.11457600555449089 chr6 171115067 3309177 0.019338899011154875 0.1701899677960969 chr7 159138663 2717019 0.01707328030021215 0.18718285717345584 chr8 146364022 3373687 0.023049974672054312 0.17196137346252435 chr9 141213431 2026667 0.014351800573417128 0.15028116635173613 chr10 135534747 2881005 0.02125657858054658 0.18683634465310495 chr11 135006516 2298474 0.017024911597600223 0.16338125345603044 chr12 133851895 2367857 0.01769012683757671 0.14291540693924373 chr13 115169878 1076837 0.00934998819743475 0.10285668637577522 chr14 107349540 1049637 0.009777750328506299 0.11218144605380811 chr15 102531392 1419748 0.013846959182998315 0.12764188723616685 chr16 90354753 1016151 0.011246237372814244 0.11899855749325516 chr17 81195210 1134547 0.013973077968515631 0.13071736195792502 chr18 78077248 909085 0.01164340474705256 0.2260594618067628 chr19 59128983 1052427 0.017798834794773993 0.19149860085032064 chr20 63025520 850923 0.013501245209876889 0.12387954998119242 chr21 48129895 435158 0.009041324523978288 0.10812220222611743 chr22 51304566 793246 0.015461508825549758 0.132230774825367 chrMT 16571 4878 0.29436968197453384 0.5696682911158499 chrX 155270560 2644463 0.01703132261518217 0.1482533890409676 chrY 59373566 116924 0.001969293877346023 0.05773125472742369